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Yorodumi- PDB-5byl: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5byl | ||||||
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Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPCP and Magnesium | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance | ||||||
Function / homology | Function and homology information aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / N-acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2016 Title: Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia. Authors: Caldwell, S.J. / Huang, Y. / Berghuis, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5byl.cif.gz | 538.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5byl.ent.gz | 442.8 KB | Display | PDB format |
PDBx/mmJSON format | 5byl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5byl_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5byl_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5byl_validation.xml.gz | 56 KB | Display | |
Data in CIF | 5byl_validation.cif.gz | 81.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byl ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byl | HTTPS FTP |
-Related structure data
Related structure data | 5iqaC 5iqbC 5iqcC 5iqdC 5iqeC 5iqfC 5iqgC 5iqhC 5iqiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | SAXS |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35948.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479 Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aacA-aphD, R015, VRA0030 / Plasmid: pET-22b-APH(2'')-Ia / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(LDE3) References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 1081 molecules
#2: Chemical | ChemComp-GCP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80-120mM MgCl2, 8% Glycerol, 10% PEG3350, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→58.92 Å / Num. obs: 82837 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Net I/av σ(I): 3.8 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.6 / % possible all: 65.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: APH(2'')-Ia GMPPNP-Mg complex Resolution: 2.15→58.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 ...Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 diverged from physiologically sensible positions, and so the single occupancy was retained, despite this clash.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→58.92 Å
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Refine LS restraints |
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